IR spectra of paracetamol

Paracetamol is a very popular medication used to treat pain and fever. IR spectra of paracetamol have been measured for powder crystals. Ab initio calculations of its equilibrium geometry and vibrational spectra were carried out for spectrum interpretation. Differences between the experimental IR spectra of crystalline samples have been analyzed. Variations of molecular structure from the isolated state to molecular crystal were estimated based on the difference between the optimized molecular parameters of free molecules and the experimental bond lengths and angles evaluated for the crystal forms of the title compounds. The role of hydrogen bonds in the structure of molecular crystals of paracetamol is investigated. Bangladesh J. Sci. Ind. Res.56(4), 255-262, 2021

Analysis of the Glycosaminoglycan Chains of Proteoglycans

Glycosaminoglycans (GAGs) are heterogeneous, negatively charged, macromolecules that are found in animal tissues. Based on the form of component sugar, GAGs have been categorized into four different families: heparin/heparan sulfate, chondroitin/dermatan sulfate, keratan sulfate, and hyaluronan. GAGs engage in biological pathway regulation through their interaction with protein ligands. Detailed structural information on GAG chains is required to further understanding of GAG–ligand interactions. However, polysaccharide sequencing has lagged behind protein and DNA sequencing due to the non-template-driven biosynthesis of glycans. In this review, we summarize recent progress in the analysis of GAG chains, specifically focusing on techniques related to mass spectroscopy (MS), including separation techniques coupled to MS, tandem MS, and bioinformatics software for MS spectrum interpretation. Progress in the use of other structural analysis tools, such as nuclear magnetic resonance (NMR) and hyphenated techniques, is included to provide a comprehensive perspective.

The Zebra Mussel (Dreissena polymorpha) as a Model Organism for Ecotoxicological Studies: A Prior 1H NMR Spectrum Interpretation of a Whole Body Extract for Metabolism Monitoring

The zebra mussel (Dreissena polymorpha) represents a useful reference organism for the ecotoxicological study of inland waters, especially for the characterization of the disturbances induced by human activities. A nuclear magnetic resonance (NMR)-based metabolomic approach was developed on this species. The investigation of its informative potential required the prior interpretation of a reference 1H NMR spectrum of a lipid-free zebra mussel extract. After the extraction of polar metabolites from a pool of whole-body D. polymorpha powder, the resulting highly complex 1D 1H NMR spectrum was interpreted and annotated through the analysis of the corresponding 2D homonuclear and heteronuclear NMR spectra. The spectrum interpretation was completed and validated by means of sample spiking with 24 commercial compounds. Among the 238 detected 1H signals, 53% were assigned, resulting in the identification of 37 metabolites with certainty or high confidence, while 5 metabolites were only putatively identified. The description of such a reference spectrum and its annotation are expected to speed up future analyses and interpretations of NMR-based metabolomic studies on D. polymorpha and to facilitate further explorations of the impact of environmental changes on its physiological state, more particularly in the context of large-scale ecological and ecotoxicological studies.

A brief introduction to the basics of NMR spectroscopy and selected examples of its applications to materials characterization

Nuclear magnetic resonance (NMR) spectroscopy is an analytical technique that gives information on the local magnetic field around atomic nuclei. Since the local magnetic field of the nucleus is directly influenced by such features of the molecular structure as constitution, configuration, conformation, intermolecular interactions, etc., NMR can provide exhaustive information on the chemical structure, which is unrivaled by any other analytical method. Starting from the 1950s, NMR spectroscopy first revolutionized organic chemistry and became an indispensable tool for the structure elucidation of small, soluble molecules. As the technique evolved, NMR rapidly conquered other disciplines of chemical sciences. When the analysis of macromolecules and solids also became feasible, the technique turned into a staple in materials characterization, too. All aspects of NMR spectroscopy, including technical and technological development, as well as its applications in natural sciences, have been growing exponentially since its birth. Hence, it would be impossible to cover, or even touch on, all topics of importance related to this versatile analytical tool. In this tutorial, we aim to introduce the reader to the basic principles of NMR spectroscopy, instrumentation, historical development and currently available brands, practical cost aspects, sample preparation, and spectrum interpretation. We show a number of advanced techniques relevant to materials characterization. Through a limited number of examples from different fields of materials science, we illustrate the immense scope of the technique in the analysis of materials. Beyond our inherently limited introduction, an ample list of references should help the reader to navigate further in the field of NMR spectroscopy.

Removing interference-based effects from infrared spectra – interference fringes re-revisited

Substantial refractive index mismatches between substrate and layers lead to undulating baselines and changes of band intensity, shape and position. For proper spectrum interpretation, all of these effects must be removed.

Measuring proteomes with long strings: A new, unconstrained paradigm in mass spectrum interpretation

SummaryThousands of protein post-translational modifications (PTMs) dynamically impact nearly all cellular functions. Mass spectrometry is well suited to PTM identification, but proteome-scale analyses are biased towards PTMs with existing enrichment methods. To measure the full landscape of PTM regulation, software must overcome two fundamental challenges: intractably large search spaces and difficulty distinguishing correct from incorrect identifications. Here, we describe TagGraph, software that overcomes both challenges with a string-based search method orders of magnitude faster than current approaches, and probabilistic validation model optimized for PTM assignments. When applied to a human proteome map, TagGraph tripled confident identifications while revealing thousands of modification types on nearly one million sites spanning the proteome. We expand known sites by orders of magnitude for highly abundant yet understudied PTMs such as proline hydroxylation, and derive tissue-specific insight into these PTMs’ roles. TagGraph expands our ability to survey the full landscape of PTM function and regulation.

Application of Neural Networks in Diagnostics of Chemical Compounds Based on their Infrared Spectra

The paper presents possibilities of using the so-called „finger-print“ identification method and artificial neural network (ANN) for diagnosis of chemical compounds. The construction of a tool specifically developed for this purpose and the ANN, as well as the required conditions for its proper functioning were described. The identification of chemical compounds was tested in two different ways for proving correctness of the assumptions. First of all, initial studies were carried out with the objective to verify the proper functioning of the developed procedure for IR spectrum interpretation. The second research stage was to find out how the properties of artificial neural networks will satisfy identification or differentiation in case of spectra with very similar structures or for mixtures consisting of several chemical compounds. Interpretation of infrared spectra of mono-constituent substances was successfully performed for both - the training and test data. Interpretation process of infrared spectra of bi-component substances, based on the example of structurally related compounds obstructing identification process, should also be described as positive. The model was able to interpret spectra of mixtures, which were previously registered into the database. Unfortunately, the program is not always able to determine which chemical substances reflect their presence in the infrared spectrum of ternary mixtures. During the research tests, it was also noted that the more complex the structure of a substance being present in the mixture was, the more difficult the interpretation of the spectra to be carry out properly by the program was. On the other hand, positive results were obtained for mixtures of compounds with not so complex structure. It must be emphasized that the results so far are promising and more attention should be paid to them in further studies.